I would say that if he has previously been a good independent sleeper, you will not 'ruin' it by staying with him while he is not feeling well, especially if you are just standing by his crib. When my DD is sick or teething bad, we usually rock with her until she is calm again and then put her back into bed. And a few times she has needed to be rocked all the way back to sleep. This has never hindered her ability to settle on her own again when she is feeling better. She just goes right back to independent sleep. I do know that some people do WIWO after their LOs are feeling better to get back to independent sleep, so if it is a problem after he's better, you can always do that too. If he is not feeling well, I would definitely not leave him to cry!